I have the exact same Case (love it in the minimalist white, but a lot of people go for the Black/Red) !!!
Also to got a similar MotherBoard (The Z97-Pro Wifi/AC. I have no ethernet ports). Basically the same thing but with wifi/ac and some unnecessary stuff.
Ultimately, you'll be fine! The fans all work, I can tell you this because I am using them now. Is there any better way to prove that they work?
The inbuilt software on the Motherboard handles it all fine, and if you really want to adjust things, then go right ahead and use the Asus BIOS software.
Honestly, you won't need to change the case or get a controller. Controllers are pretty unnecessary anyway.
Oh and another thing, the NZXT H440 is a great case. I myself went through about 25 odd cases until I found one I liked, and if you are going to WaterCool, and move to the new "digital" era. Then the H440 is one of the best cases to get. It's made from a sturdy aluminium. It has a fair amount of room, and a dedicated PSU holding area. It comes with all the fans which is great, and it looks pretty awesome.
I wouldn't change the case if I were you, nor the Motherboard either.